.. _backbone-label:

Masurca
==============================

Introduction
~~~~~~~~
The MaSuRCA (Maryland Super Read Cabog Assembler) genome assembly and analysis toolkit contains of MaSuRCA genome assembler, QuORUM error corrector for Illumina data, POLCA genome polishing software, Chromosome scaffolder, jellyfish mer counter, and MUMmer aligner.


| For more information, please check:
| Docker hub: https://hub.docker.com/r/staphb/masurca 
| Home page: https://github.com/alekseyzimin/masurca

.. note::
    Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions
~~~~~~~
.. list-table::
  :width: 100 %
  :widths: 25 75
  :header-rows: 1

  * - Cluster
    - Version(s)

  * - ANVIL
    - 4.0.9, 4.1.0
  * - BELL
    - 4.0.9, 4.1.0
  * - GAUTSCHI
    - 4.0.9, 4.1.0
  * - NEGISHI
    - 4.0.9, 4.1.0
  * - SCHOLAR
    - 4.0.9, 4.1.0

Commands
~~~~~~~
- masurca
- build_human_reference.sh
- chromosome_scaffolder.sh
- close_gaps.sh
- close_scaffold_gaps.sh
- correct_with_k_unitigs.sh
- deduplicate_contigs.sh
- deduplicate_unitigs.sh
- eugene.sh
- extract_chrM.sh
- filter_library.sh
- final_polish.sh
- fix_unitigs.sh
- fragScaff.sh
- mega_reads_assemble_cluster.sh
- mega_reads_assemble_cluster2.sh
- mega_reads_assemble_polish.sh
- mega_reads_assemble_ref.sh
- parallel_delta-filter.sh
- polca.sh
- polish_with_illumina_assembly.sh
- recompute_astat_superreads.sh
- recompute_astat_superreads_CA8.sh
- reconcile_alignments.sh
- refine.sh
- resolve_trio.sh
- run_ECR.sh
- samba.sh
- splitScaffoldsAtNs.sh

Module
~~~~~~~~
You can load the modules by::

    module load biocontainers
    module load masurca

Example job
~~~~~
.. warning::
    Using ``#!/bin/sh -l`` as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use ``#!/bin/bash`` instead.

To run masurca on our clusters:

.. tab-set::

  .. tab-item:: Anvil

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A myallocation     # Allocation name
        #SBATCH -p wholenode        # Partition name
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=masurca
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers masurca

        # Your masurca workflow...

  .. tab-item:: Bell, Gautschi, or Negishi

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A mygroup     # Group name
        #SBATCH -p cpu         # Partition name
        #SBATCH -q normal      # QOS name (optional)
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=masurca
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers masurca

        # Your masurca workflow...

  .. tab-item:: Gautschi-AI

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A mygroup     # Group name
        #SBATCH -p ai          # Partition name
        #SBATCH --gres=gpu:1   # Number of GPUs
        #SBATCH -q normal      # QOS name (optional)
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=masurca
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers masurca

        # Your masurca workflow...

  .. tab-item:: Gilbreth

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A mygroup     # Group name
        #SBATCH -p a100        # Partition name
        #SBATCH --gres=gpu:1   # Number of GPUs
        #SBATCH --mem=2G       # Memory
        #SBATCH -q normal      # QOS name (optional)
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=masurca
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers masurca

        # Your masurca workflow...

  .. tab-item:: Scholar

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A queue     # Queue name
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=masurca
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers masurca

        # Your masurca workflow...